LAMMPS (15 Jun 2020)
# Demonstrate MLIAP interface to quadratic SNAP potential

# Initialize simulation

variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units		metal

# generate the box and atom positions using a BCC lattice

variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4

boundary	p p p

lattice         bcc $a
lattice         bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
region		box block 0 ${nx} 0 ${ny} 0 ${nz}
region		box block 0 4 0 ${ny} 0 ${nz}
region		box block 0 4 0 4 0 ${nz}
region		box block 0 4 0 4 0 4
create_box	1 box
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 128 atoms
  create_atoms CPU = 0.000 seconds
displace_atoms  all random 0.01 0.01 0.01 12345

mass 1 183.84

# choose potential

include W.quadratic.mliap
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74

# Specify hybrid with SNAP and ZBL

pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
SNAP keyword rcutfac 4.73442 
SNAP keyword twojmax 6 
SNAP keyword nelems 1 
SNAP keyword elems W 
SNAP keyword radelems 0.5 
SNAP keyword welems 1 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword bzeroflag 1 
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 74 ${zblz}
pair_coeff 1 1 zbl 74 74
pair_coeff * * mliap W


# Setup output

compute  eatom all pe/atom
compute  energy all reduce sum c_eatom

compute  satom all stress/atom NULL
compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)

thermo_style    custom step temp epair c_energy etotal press v_press
thermo		10
thermo_modify norm yes

# Set up NVE run

timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check no

# Run MD

velocity all create 300.0 4928459 loop geom
fix 1 all nve
run             ${nsteps}
run             100
Neighbor list info ...
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.8
  ghost atom cutoff = 5.8
  binsize = 2.9, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair zbl, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (2) pair mliap, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.093 | 6.093 | 6.093 Mbytes
Step Temp E_pair c_energy TotEng Press v_press 
       0          300   -1.1602728   -1.1602728   -1.1217977     600047.3    -600047.3 
      10    288.46387   -1.1587932   -1.1587932   -1.1217976    600359.75   -600359.75 
      20    268.69718   -1.1562579   -1.1562579   -1.1217974    600870.22   -600870.22 
      30    243.19855   -1.1529874   -1.1529874   -1.1217971     601511.5    -601511.5 
      40    215.13122   -1.1493875   -1.1493875   -1.1217969    602202.36   -602202.36 
      50    187.82673   -1.1458855   -1.1458855   -1.1217966    602860.26   -602860.26 
      60    164.26822   -1.1428639   -1.1428639   -1.1217965    603413.25   -603413.25 
      70    146.65179   -1.1406045   -1.1406045   -1.1217964    603809.35   -603809.35 
      80    136.10769   -1.1392522   -1.1392522   -1.1217964    604022.32   -604022.32 
      90    132.62756    -1.138806    -1.138806   -1.1217964    604053.33   -604053.33 
     100    135.19841   -1.1391358   -1.1391358   -1.1217966    603928.48   -603928.48 
Loop time of 1.69996 on 1 procs for 100 steps with 128 atoms

Performance: 2.541 ns/day, 9.444 hours/ns, 58.825 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.6676     | 1.6676     | 1.6676     |   0.0 | 98.09
Neigh   | 0.03029    | 0.03029    | 0.03029    |   0.0 |  1.78
Comm    | 0.001238   | 0.001238   | 0.001238   |   0.0 |  0.07
Output  | 0.000452   | 0.000452   | 0.000452   |   0.0 |  0.03
Modify  | 0.000175   | 0.000175   | 0.000175   |   0.0 |  0.01
Other   |            | 0.000241   |            |       |  0.01

Nlocal:    128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3712 ave 3712 max 3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  7424 ave 7424 max 7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7424
Ave neighs/atom = 58
Neighbor list builds = 100
Dangerous builds not checked

Total wall time: 0:00:01
